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. 2024 Oct 22;11(1):1163.
doi: 10.1038/s41597-024-04014-4.

Comprehensive sequencing of the genome and transcriptome of the Xishuangbanna game fowl

Huimin Qiu #  1 , Tiao Ning #  1 , Weijun Gong  2 , Hao Sun  3 , Gui Mu  4 , Jing Li  5
Affiliations

Comprehensive sequencing of the genome and transcriptome of the Xishuangbanna game fowl

Huimin Qiu et al. Sci Data. .

Abstract

The Xishuangbanna game fowl, a local Chinese chicken breed renowned for its athleticism, is facing extinction. Despite its significance, research on its genome assembly and resequencing remains sparse, limiting our understanding of its genetic structure and function. In this study, we assembled a chromosome-level genome using second-generation sequencing and high-throughput chromosome conformation capture (Hi-C), along with transcriptome sequencing. We also resequenced 62 individuals. The resulting assembly yielded a 1.09 gigabase (Gb) high-quality genome, 994.34 Gb of resequencing data, and 141.38 Gb of transcriptome data from 15 tissues. This comprehensive dataset provides valuable insights into the artificial selection processes shaping the breed and offers a solid foundation for further genetic and population studies.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Sequencing techniques applied to Xishuangbanna game fowl, detailing the collection sites and individuals from various pedigrees.
Fig. 2
Fig. 2
Hi-C interaction heat map in Xishuangbanna game fowl.
Fig. 3
Fig. 3
Quality assessment of Hi-C data (a), Illumina sequencing (b), resequencing (c), and transcriptome sequencing (d) data.
Fig. 4
Fig. 4
Genome assembly and quality assessment workflow for Xishuangbanna game fowl.
Fig. 5
Fig. 5
Synteny Analysis Between Game fowl and GGswu1 Chromosomes. (a) Synteny analysis for chromosomes >10 Mb, including 20 autosomes and the W and Z sex chromosomes. Different colors represent different chromosomes, with lines indicating syntenic regions between species. (b) Synteny analysis for microchromosomes <10 Mb. Different colors indicate different microchromosomes, with lines displaying syntenic regions.
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